Nature Communications - 19 June 2013

Advertisement Combining open-access publishing with a powerful networking platform. The Frontiers publication process and Research Networking Platform allow you to build your own scientific profiles while following the work of colleagues, mentors and your science heroes. Connect with your community today     Weekly Content Alert 19 June 2013  Featured image: Ito et al. show that a mechanically induced phase transformation between polymorphs proceeds via a single-crystal-to-single-crystal molecular dominoes-type mechanism. Latest content: Articles Journal homepage Recommend to library Web feed   Advertisement Ludwig Institute for Cancer Research, Nature Genetics, and Nature Reviews Cancer present: Nuclear Reprogramming and the Cancer Genome St. Catherine's College, University of Oxford, Oxford, UK September 25-27, 2013 Click here for more information or to register for this conference today!     Latest Articles View all Articles     Immunologic and chemical targeting of the tight-junction protein Claudin-6 eliminates tumorigenic human pluripotent stem cells Uri Ben-David, Neta Nudel and Nissim Benvenisty The potential tumorigenicity of human pluripotent stem cells (hPSCs) limits their application in cell therapies. Ben-David et al. identify the tight-junction protein Claudin-6 as a cell-surface marker of hPSCs, and demonstrate three Claudin-6-based strategies to remove tumorigenic hPSCs from mixed cell cultures. 18 June 2013 | doi: 10.1038/ncomms2992 Biological Sciences  Cell biology  An earthquake gap south of Istanbul Marco Bohnhoff, Fatih Bulut, Georg Dresen, Peter E. Malin, Tuna Eken and Mustafa Aktar The North Anatolian Fault Zone in Turkey has produced many large earthquakes, however the Marmara region has been inactive and is facing a high probability for a large earthquake. Here, Bohnhoff et al. report on a large seismicity gap in this area with implications for a seismic hazard for Istanbul. 18 June 2013 | doi: 10.1038/ncomms2999 Earth Sciences  Geology and geophysics  Cortical responses elicited by photovoltaic subretinal prostheses exhibit similarities to visually evoked potentials Yossi Mandel, Georges Goetz, Daniel Lavinsky, Philip Huie, Keith Mathieson, Lele Wang, Theodore Kamins, Ludwig Galambos, Richard Manivanh, James Harris and Daniel Palanker Visual prosthetics based on photovoltaic devices have been proposed to allow the functional restoration of lost sight. Mandel et al. assess the retinal responses to implanted retinal prosthetics in rats with degenerate retinas and find that they elicit responses in the visual cortex when stimulated by light. 18 June 2013 | doi: 10.1038/ncomms2980 Biological Sciences  Medical research  Neuroscience  Exceptionally well-preserved Cretaceous microfossils reveal new biomineralization styles Jens E. Wendler and Paul Bown Well-preserved calcareous microfossils are rare but required for proof of biological affinity and as paleoclimatic proxies. Here the authors present extinct plankton fossils with biomineralogical structures of previously unseen complexity, possibly related to modern dinoflagellates. 18 June 2013 | doi: 10.1038/ncomms3052 Biological Sciences  Palaeontology  Upper mantle viscosity and dynamic subsidence of curved continental margins Victor Sacek and Naomi Ussami The evolution of continental rifting curvature can be studied using thermal convection models. Studying how this curvature controls the subsidence of offshore basins, Sacek and Ussami find that the mantle viscosity structure affects the subsidence rate and evolution of sedimentary basins along curved margins. 18 June 2013 | doi: 10.1038/ncomms3036 Earth Sciences  Geology and geophysics  Mitochondrial calcium uniporter Mcu controls excitotoxicity and is transcriptionally repressed by neuroprotective nuclear calcium signals OPEN Jing Qiu, Yan-Wei Tan, Anna M. Hagenston, Marc-Andre Martel, Niclas Kneisel, Paul A. Skehel, David J. A. Wyllie, Hilmar Bading and Giles E. Hardingham Calcium uptake by the mitochondrial calcium uniporter is implicated in excitotoxicity. This study shows that the uniporter gene product mediates mitochondrial calcium uptake and depolarisation in neurons during excitotoxicity, and is transcriptionally repressed by neuroprotective nuclear calcium signals. 18 June 2013 | doi: 10.1038/ncomms3034 Biological Sciences  Cell biology  Neuroscience  BDNF–TrkB signaling in striatopallidal neurons controls inhibition of locomotor behavior Dario Besusso, Mirjam Geibel, Dana Kramer, Tomasz Schneider, Valentina Pendolino, Barbara Picconi, Paolo Calabresi, David M. Bannerman and Liliana Minichiello The neurotrophic factor BDNF is implicated in striatal cell long-term survival. Besusso et al. selectively delete BDNF receptors in the striatal circuitry of mice and find that this leads to hyperlocomotion, which is associated with dopamine receptor-dependent increases in specific kinases. 18 June 2013 | doi: 10.1038/ncomms3031 Biological Sciences  Neuroscience  Photolatently modulable hydrogels using unilamellar titania nanosheets as photocatalytic crosslinkers Mingjie Liu, Yasuhiro Ishida, Yasuo Ebina, Takayoshi Sasaki and Takuzo Aida Postsynthetic modulation of the structural properties of hydrogels is desirable for a range of biomaterials applications. Here, the authors fabricate photolatently modulable polymer hydrogels crosslinked by titania nanosheets, which may be micropatterned with high spatial and temporal resolution. 18 June 2013 | doi: 10.1038/ncomms3029 Chemical Sciences  Materials science  Implementation of generalized quantum measurements for unambiguous discrimination of multiple non-orthogonal coherent states F. E. Becerra, J. Fan and A. Migdall Discriminating non-orthogonal quantum states is far from simple due to the inherent measurement difficulties of quantum mechanics. Becerra et al. present a scheme enabling unambiguous discrimination of four non-orthogonal coherent states that outperforms conventional measurements under realistic conditions. 18 June 2013 | doi: 10.1038/ncomms3028 Physical Sciences  Applied physics  Optical physics  Robust site-resolvable quantum gates in an optical lattice via inhomogeneous control J. H. Lee, E. Montano, I. H. Deutsch and P. S. Jessen Ultracold atoms in optical lattices are promising for quantum information applications, but it is important to address individual sites with high accuracy and low cross-talk. Lee et al. adapt inhomogeneous control methods to improve the performance of single-qubit gates for selected sites. 18 June 2013 | doi: 10.1038/ncomms3027 Physical Sciences  Atomic and molecular physics  Optical physics  Spin readout and addressability of phosphorus-donor clusters in silicon H. Büch, S. Mahapatra, R. Rahman, A. Morello and M. Y. Simmons The spin of an electron bound to a single phosphorus atom in silicon is of interest for spin-based electronics such as quantum computing. Here, Büch et al. show these spin properties are retained even for clusters of a few phosphorus atoms, providing an additional means for quantum bit addressability. 18 June 2013 | doi: 10.1038/ncomms3017 Physical Sciences  Applied physics  Condensed matter  Nanotechnology  A regulatory role for Staphylococcus aureus toxin–antitoxin system PemIKSa Michal Bukowski, Robert Lyzen, Weronika M. Helbin, Emilia Bonar, Agnieszka Szalewska-Palasz, Grzegorz Wegrzyn, Grzegorz Dubin, Adam Dubin and Benedykt Wladyka A role of toxin–antitoxin systems in global regulation of bacterial gene expression has been proposed. Bukowski et al. now demonstrate that a novel toxin–antitoxin system from S. aureus encodes an endoribonuclease that regulates virulence gene expression by targeting translation. 18 June 2013 | doi: 10.1038/ncomms3012 Biological Sciences  Microbiology  Emergence of bimodality in controlling complex networks Tao Jia, Yang-Yu Liu, Endre Csóka, Márton Pósfai, Jean-Jacques Slotine and Albert-László Barabási The control of a complex network can be achieved by different combinations of relatively few driver nodes. Tao Jia and colleagues show that this can lead to two distinct control modes–centralized or distributed–that determine the number of nodes that can act as driver node. 18 June 2013 | doi: 10.1038/ncomms3002 Physical Sciences  Theoretical physics  Two distinct secretion systems facilitate tissue invasion by the rice blast fungus Magnaporthe oryzae OPEN Martha C. Giraldo, Yasin F. Dagdas, Yogesh K. Gupta, Thomas A. Mentlak, Mihwa Yi, Ana Lilia Martinez-Rocha, Hiromasa Saitoh, Ryohei Terauchi, Nicholas J. Talbot and Barbara Valent Understanding how fungal pathogens deliver proteins to diverse plant compartments is critical for developing disease control. Giraldo et al. demonstrate that the blast fungus possesses distinct secretion systems for proteins targeted to compartments inside or outside living rice cells. 18 June 2013 | doi: 10.1038/ncomms2996 Biological Sciences  Microbiology  Plant sciences  Fork sensing and strand switching control antagonistic activities of RecQ helicases OPEN Daniel Klaue, Daniela Kobbe, Felix Kemmerich, Alicja Kozikowska, Holger Puchta and Ralf Seidel RecQ helicases are enzymes that play a central role in maintaining genome stability in the DNA repair cascade. Klaue et al. show that RecQ2 and RecQ3 from Arabidopsis thaliana process DNA by, respectively, unwinding and rewinding forked DNA substrates, using a frequent strand switching mechanism. 17 June 2013 | doi: 10.1038/ncomms3024 Biological Sciences  Biophysics  Molecular biology  Plant sciences  Dynamical spin–orbital correlation in the frustrated magnet Ba3CuSb2O9 Yuki Ishiguro, Kenta Kimura, Satoru Nakatsuji, Satoshi Tsutsui, Alfred Q. R. Baron, Tsuyoshi Kimura and Yusuke Wakabayashi Spin–orbital quantum liquids are exotic quantum phases in frustrated magnets that arise if frustrated spin and orbital degrees of freedom are coupled. Here, the authors find a dynamical spin–orbital state in the frustrated magnet Ba3CuSb2O9, which indicates the formation of a spin–orbital quantum liquid. 17 June 2013 | doi: 10.1038/ncomms3022 Physical Sciences  Condensed matter  Broadly tunable terahertz generation in mid-infrared quantum cascade lasers Karun Vijayraghavan, Yifan Jiang, Min Jang, Aiting Jiang, Karthik Choutagunta, Augustinas Vizbaras, Frederic Demmerle, Gerhard Boehm, Markus C. Amann and Mikhail A. Belkin Compact, tunable terahertz sources are highly desired for sensing and imaging applications. Here Vijayraghavan et al. demonstrate room-temperature quantum cascade laser sources based on the non-linear optical conversion of mid-infrared light that provide a tunable output over a 3.5-THz bandwidth. 17 June 2013 | doi: 10.1038/ncomms3021 Physical Sciences  Applied physics  Optical physics  Fibroblast growth factor 21 protects against cardiac hypertrophy in mice A. Planavila, I. Redondo, E. Hondares, M. Vinciguerra, C. Munts, R. Iglesias, L. A. Gabrielli, M. Sitges, M. Giralt, M. van Bilsen and F. Villarroya Fibroblast growth factor 21 (FGF21) regulates energy metabolism in peripheral tissues. Here Planavila and colleagues show that FGF21 also acts directly on cardiomyocytes, thereby protecting mice against cardiac hypertrophy. 17 June 2013 | doi: 10.1038/ncomms3019 Biological Sciences  Biochemistry  Medical research  Automated long-term tracking and social behavioural phenotyping of animal colonies within a semi-natural environment Aharon Weissbrod, Alexander Shapiro, Genadiy Vasserman, Liat Edry, Molly Dayan, Assif Yitzhaky, Libi Hertzberg, Ofer Feinerman and Tali Kimchi Quantification of the behavioural phenotype of animals within a group requires simultaneous position and identity tracking of multiple individuals. Here the authors report an automated tracking system that combines video- and RFID-tracking data and allows behavioural phenotyping of uniquely identified group-living animals. 17 June 2013 | doi: 10.1038/ncomms3018 Biological Sciences  Neuroscience  Lagrangian scale of particle dispersion in turbulence Hua Xia, Nicolas Francois, Horst Punzmann and Michael Shats A better understanding of many environmental phenomena, such as plankton spreading in the ocean, relies on knowledge of the dispersion statistics. Xia et al. trace particles' trajectories in laboratory turbulence and reveal that a single force scale can be sufficient to predict the dispersion of particles. 17 June 2013 | doi: 10.1038/ncomms3013 Physical Sciences  Fluids and plasma physics  Two-barrier stability that allows low-power operation in current-induced domain-wall motion Kab-Jin Kim, Ryo Hiramatsu, Tomohiro Koyama, Kohei Ueda, Yoko Yoshimura, Daichi Chiba, Kensuke Kobayashi, Yoshinobu Nakatani, Shunsuke Fukami, Michihiko Yamanouchi, Hideo Ohno, Hiroshi Kohno, Gen Tatara and Teruo Ono Controlling magnetic domain wall motion in nanowires requires a thorough knowledge of the depinning mechanisms. Here, the authors show that current-induced intrinsic depinning has a different energy barrier than magnetic field-induced extrinsic depinning, and succeed in quantifying the respective barriers. 17 June 2013 | doi: 10.1038/ncomms3011 Physical Sciences  Materials science  Nanotechnology  Myosin Vb controls biogenesis of post-Golgi Rab10 carriers during axon development Yang Liu, Xiao-Hui Xu, Qi Chen, Tong Wang, Cai-Yun Deng, Bao-Liang Song, Jiu-Lin Du and Zhen-Ge Luo Polarized membrane addition during axon development requires post-Golgi Rab10 carriers, whose biogenesis mechanisms remain unknown. This work shows that specific interaction between Rab10 and MYO5B controls formation of the Rab10 carriers, and this process is essential for neuronal polarization. 17 June 2013 | doi: 10.1038/ncomms3005 Biological Sciences  Cell biology  Developmental biology  Neuroscience  Ultrafast collinear scattering and carrier multiplication in graphene D. Brida, A. Tomadin, C. Manzoni, Y. J. Kim, A. Lombardo, S. Milana, R. R. Nair, K. S. Novoselov, A. C. Ferrari, G. Cerullo and M. Polini Investigation of the initial stages of the interaction of light with carriers in graphene is challenging. Here, the authors probe the process with ultrafast pump-probe spectroscopy and microscopic theory, and observe the role of collinear scattering, which gives rise to Auger processes, including carrier multiplication. 17 June 2013 | doi: 10.1038/ncomms2987 Physical Sciences  Condensed matter  Materials science  Optical physics  A molecular explanation for the recessive nature of parkin–linked Parkinson's disease OPEN Donald E. Spratt, R. Julio Martinez-Torres, Yeong J. Noh, Pascal Mercier, Noah Manczyk, Kathryn R. Barber, Jacob D. Aguirre, Lynn Burchell, Andrew Purkiss, Helen Walden and Gary S. Shaw Mutations in the E3 ubiquitin ligase parkin are associated with juvenile Parkinson's disease. Here the authors report the solution structure of the Parkin RING2 domain, revealing how disease-associated mutations affect its function and providing a molecular explanation for the recessive nature of the disease. 17 June 2013 | doi: 10.1038/ncomms2983 Biological Sciences  Biochemistry  Neuroscience  Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases OPEN B.E. Riley, J.C. Lougheed, K. Callaway, M. Velasquez, E. Brecht, L. Nguyen, T. Shaler, D. Walker, Y. Yang, K. Regnstrom, L. Diep, Z. Zhang, S. Chiou, M. Bova, D.R. Artis, N. Yao, J. Baker, T. Yednock and J.A. Johnston The Parkinson's disease-associated protein Parkin regulates the fate of damaged mitochondria by ubiquitinating mitochondrial substrates. Riley et al. present the crystal structure of the Parkin-R0RBR domain, providing new insight into the catalytic mechanism of the enzyme. 17 June 2013 | doi: 10.1038/ncomms2982 Biological Sciences  Biochemistry  Neuroscience  Mechanism of microtubule array expansion in the cytokinetic phragmoplast OPEN Takashi Murata, Toshio Sano, Michiko Sasabe, Shigenori Nonaka, Tetsuya Higashiyama, Seiichiro Hasezawa, Yasunori Machida and Mitsuyasu Hasebe Plant cell division is driven by the expansion of the phragmoplast, a characteristic structure that forms in the middle of the plant cell during cytokinesis. Murata et al. use genetic and cell imaging approaches to clarify the microtubule behaviour that leads to phragmoplast expansion. 17 June 2013 | doi: 10.1038/ncomms2967 Biological Sciences  Cell biology  Plant sciences  Arabidopsis FLC clade members form flowering-repressor complexes coordinating responses to endogenous and environmental cues OPEN Xiaofeng Gu, Chau Le, Yizhong Wang, Zicong Li, Danhua Jiang, Yuqi Wang and Yuehui He Flowering time is a critical developmental transition for a plant's reproductive success and it depends on endogenous and environmental signals. Here Gu et al. show that MADS-domain floral repressors form protein complexes that coordinate Arabidopsis responses to these cues and regulate its flowering time. 17 June 2013 | doi: 10.1038/ncomms2947 Biological Sciences  Molecular biology  Plant sciences  Genome of the red alga Porphyridium purpureum Debashish Bhattacharya, Dana C. Price, Cheong Xin Chan, Huan Qiu, Nicholas Rose, Steven Ball, Andreas P. M. Weber, Maria Cecilia Arias, Bernard Henrissat, Pedro M. Coutinho, Anagha Krishnan, Simone Zäuner, Shannon Morath, Frédérique Hilliou, Andrea Egizi, Marie-Mathilde Perrineau and Hwan Su Yoon Red algae form one of the most ancient eukaryotic lineages, and have undergone multiple symbioses. Here, Price et al. report the first genome sequence for a mesophilic red alga, and reveal significant differences between these organisms and hyperthermopilic algae. 17 June 2013 | doi: 10.1038/ncomms2931 Biological Sciences  Microbiology  Quantum fluctuations in spin-ice-like Pr2Zr2O7 K. Kimura, S. Nakatsuji, J-J. Wen, C. Broholm, M. B. Stone, E. Nishibori and H. Sawa Although attempts to identify magnetic monopoles in free space have been unsuccessful, monopole-like particles with classical dynamics have been reported in magnetic materials called spin ice. Kimura et al. identify quantum fluctuations of monopolar character in a new type of spin ice, Pr2Zr2O7 17 June 2013 | doi: 10.1038/ncomms2914 Physical Sciences  Condensed matter  Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization Avelino Javer, Zhicheng Long, Eileen Nugent, Marco Grisi, Kamin Siriwatwetchakul, Kevin D. Dorfman, Pietro Cicuta and Marco Cosentino Lagomarsino The spatial and temporal organization of bacterial chromosomes is important for many cellular functions. Using high-precision measurements of fluorescently labelled chromosomal loci, Javer et al. demonstrate variation in the dynamics of different chromosomal sites, which may either be due to differential organization of the chromosome or spatial variation in molecular noise. 14 June 2013 | doi: 10.1038/ncomms3003 Biological Sciences  Cell biology  Microbiology  Mechanical stimulation and solid seeding trigger single-crystal-to-single-crystal molecular domino transformations Hajime Ito, Mai Muromoto, Sayaka Kurenuma, Shoji Ishizaka, Noboru Kitamura, Hiroyasu Sato and Tomohiro Seki Despite extensive research on mechanical control of phase change in crystals, a molecular-level understanding of the forces involved is lacking. Here, the authors observe a phase change process optically, and show that it is induced by mechanical stimulation and proceeds through domino-like self-replication. 14 June 2013 | doi: 10.1038/ncomms3009 Chemical Sciences  Inorganic chemistry  Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells OPEN Parul Mehta, Goran Jovanovic, Tchern Lenn, Andreas Bruckbauer, Christoph Engl, Liming Ying and Martin Buck Cellular adaptive responses require temporal and spatial control of key regulatory protein complexes. Mehta et al. describe the dynamic interaction of a transcriptional activator mediating membrane stress response in E. coli with its negative regulator, the cell membrane and the transcription machinery. 14 June 2013 | doi: 10.1038/ncomms2997 Biological Sciences  Microbiology  Molecular biology  A solid with a hierarchical tetramodal micro-meso-macro pore size distribution OPEN Yu Ren, Zhen Ma, Russell E. Morris, Zheng Liu, Feng Jiao, Sheng Dai and Peter G. Bruce Porous solids have potential applications in energy storage, gas separation and catalysis technologies. Here, the authors report a hierarchical solid with porosity spanning the micro, meso and macro ranges, which is synthesized using templating silica, and potassium ions as both templates and reactive species. 14 June 2013 | doi: 10.1038/ncomms3015 Chemical Sciences  Inorganic chemistry  Materials science  A ladder polysilane as a template for folding palladium nanosheets Yusuke Sunada, Ryohei Haige, Kyohei Otsuka, Soichiro Kyushin and Hideo Nagashima Since the isolation of graphene, there has been extensive interest in other two-dimensional structures including metallic nanosheets. Here, the authors report the use of ladder polysilane ligands for the synthesis of palladium clusters containing eleven metal ions, made up of two heptametallic nanosheets. 14 June 2013 | doi: 10.1038/ncomms3014 Chemical Sciences  Inorganic chemistry  Giant cationic polyelectrolytes generated via electrochemical oxidation of single-walled carbon nanotubes Stephen A. Hodge, Mustafa K. Bayazit, Hui Huang Tay and Milo S. P. Shaffer Reduced carbon nanotube anions can be effectively processed and functionalized. Here, the authors prepare discrete nanotube cations by electrochemical oxidation, and the confirmation of their reactivity towards nucleophiles suggests a new library of covalent nanotube modifications. 14 June 2013 | doi: 10.1038/ncomms2989 Chemical Sciences  Nanotechnology  Organic chemistry  Identification and optimization of small-molecule agonists of the human relaxin hormone receptor RXFP1 Jingbo Xiao, Zaohua Huang, Catherine Z. Chen, Irina U. Agoulnik, Noel Southall, Xin Hu, Raisa E. Jones, Marc Ferrer, Wei Zheng, Alexander I. Agoulnik and Juan J. Marugan The peptide hormone relaxin has potential in the treatment of acute heart failure, but it must be intravenously injected and has a short half-life after administration. Now, small-molecule alternatives to relaxin are reported with similar efficacies to the natural hormone in functional assays. 14 June 2013 | doi: 10.1038/ncomms2953 Chemical Sciences  Chemical biology  Medicinal chemistry  Model-based rational design of an oncolytic virus with improved therapeutic potential Fabrice Le Bœuf, Cory Batenchuk, Markus Vähä-Koskela, Sophie Breton, Dominic Roy, Chantal Lemay, Julie Cox, Hesham Abdelbary, Theresa Falls, Girija Waghray, Harold Atkins, David Stojdl, Jean-Simon Diallo, Mads Kœrn and John C. Bell Oncolytic viruses can serve as self-replicating anticancer agents. Le Bœuf et al. combine synthetic modelling and molecular biology approaches to create a virus with enhanced oncolytic activity in vitro and in vivo due to its expression of an interferon antagonist. 14 June 2013 | doi: 10.1038/ncomms2974 Biological Sciences  Medical research  Systems biology  Virology  Uncovering loss mechanisms in silver nanoparticle-blended plasmonic organic solar cells Bo Wu, Xiangyang Wu, Cao Guan, Kong Fai Tai, Edwin Kok Lee Yeow, Hong Jin Fan, Nripan Mathews and Tze Chien Sum Metallic nanoparticles are commonly used to facilitate light trapping in organic solar cells, but they can also reduce cell performance. Wu et al. demonstrate that a trap-assisted recombination of charge carriers leads to degradation, irrespective of an initially enhanced absorption and excitation. 13 June 2013 | doi: 10.1038/ncomms3004 Physical Sciences  Condensed matter  Nanotechnology  Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines OPEN Johann Elbaz, Alessandro Cecconello, Zhiyuan Fan, Alexander O. Govorov and Itamar Willner DNA nanotechnology, including DNA machines and devices for computing, is a rapidly expanding field of research. Here, the authors fabricate DNA catenane machines for the programmable arrangement of gold nanoparticle cargoes, and study their switchable spectroscopic features. 13 June 2013 | doi: 10.1038/ncomms3000 Chemical Sciences  Nanotechnology  Multistep kinetic self-assembly of DNA-coated colloids Lorenzo Di Michele, Francesco Varrato, Jurij Kotar, Simon H. Nathan, Giuseppe Foffi and Erika Eiser The final state of self-assembled systems is determined by both their thermodynamic and kinetic pathways. Di Michele et al. develop a strategy to realize predesigned amorphous structures of complex DNA colloidal mixtures by selectively activating local inter- or intra-species interactions upon freezing. 13 June 2013 | doi: 10.1038/ncomms3007 Physical Sciences  Condensed matter  Materials science  Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs OPEN Daisuke Mayumi, Jan Dolfing, Susumu Sakata, Haruo Maeda, Yoshihiro Miyagawa, Masayuki Ikarashi, Hideyuki Tamaki, Mio Takeuchi, Cindy H. Nakatsu and Yoichi Kamagata Deep subsurface formations are potential sites for carbon capture and storage but how subsurface microbial communities may respond to this is not clear. Here, Mayumi et al. construct microcosms and show that increasing CO2 partial pressure via carbon capture and storage more than doubles the rate of methanogenesis. 13 June 2013 | doi: 10.1038/ncomms2998 Earth Sciences  Biogeochemistry  Ultrafast tristable spin memory of a coherent polariton gas R. Cerna, Y. Léger, T.K. Paraïso, M. Wouters, F. Morier-Genoud, M.T. Portella-Oberli and B. Deveaud The coherent control of an exciton-polariton gas would enable a variety of spin- or light-based devices. Cerna et al. optically control the spin of semiconductor polaritons in both the bistable and tristable regimes, realising an ultrafast all-optical spin memory. 13 June 2013 | doi: 10.1038/ncomms3008 Physical Sciences  Condensed matter  Nanotechnology  Optical physics  Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis Haiyun Gan, Lu Wen, Shangying Liao, Xiwen Lin, Tingting Ma, Jun Liu, Chun-xiao Song, Min Wang, Chuan He, Chunsheng Han and Fuchou Tang Changes in DNA methylation during mammalian spermatogenesis are poorly understood. The authors show that the content of 5-hydroxymethylcytosine, a stable intermediate of DNA demethylation, changes dynamically during mouse spermatogenesis and is associated with functional genomic regions and transcription. 13 June 2013 | doi: 10.1038/ncomms2995 Biological Sciences  Developmental biology  Molecular biology  Synthetic regimes due to packing constraints in dendritic molecules confirmed by labelling experiments Baozhong Zhang, Hao Yu, A. Dieter Schlüter, Avraham Halperin and Martin Kröger Classical theory predicts that branching defects are unavoidable in large dendritic molecules when steric congestion becomes important. Zhang et al. present the first direct evidence of this effect by means of defect labelling of a homologous series of dendronized polymers. 13 June 2013 | doi: 10.1038/ncomms2993 Chemical Sciences  Materials science  Cyclic electron flow is redox-controlled but independent of state transition OPEN Hiroko Takahashi, Sophie Clowez, Francis-André Wollman, Olivier Vallon and Fabrice Rappaport The switch from linear to cyclic electron flow has long been thought to rely on the migration of antenna proteins from Photosystem II to Photosystem I. Takahashi et al. report that this is not the case and that cyclic electron flow is tuned by the intrachloroplastic redox power. 13 June 2013 | doi: 10.1038/ncomms2954 Biological Sciences  Biochemistry  Biophysics  Suppression of electron–vibron coupling in graphene nanoribbons contacted via a single atom Joost van der Lit, Mark P. Boneschanscher, Daniël Vanmaekelbergh, Mari Ijäs, Andreas Uppstu, Mikko Ervasti, Ari Harju, Peter Liljeroth and Ingmar Swart Graphene nanostructures have a tremendous potential for electronic applications, although contacting them with atomic precision remains a challenge. Here, van der Lit and colleagues achieve contacting graphene nanoribbons via only a single atom, without affecting its electronic structure. 12 June 2013 | doi: 10.1038/ncomms3023 Physical Sciences  Condensed matter  Nanotechnology  Dual origin of defect magnetism in graphene and its reversible switching by molecular doping R.R. Nair, I.-L. Tsai, M. Sepioni, O. Lehtinen, J. Keinonen, A.V. Krasheninnikov, A.H. Castro Neto, M.I. Katsnelson, A.K. Geim and I.V. Grigorieva Local magnetic properties that can be controlled by an applied electric field are desirable for spintronics applications. Nair et al. show that tuning carrier concentration by molecular doping or electric field can be used to control adatoms magnetism on graphene, enabling magnetic moments to be switched on and off. 12 June 2013 | doi: 10.1038/ncomms3010 Physical Sciences  Materials science  Nanotechnology  Quantum nuclear dynamics in the photophysics of diamondoids Christopher E. Patrick and Feliciano Giustino The physical origin of the electronic properties of diamondoids has been difficult to resolve, even by advanced many-body calculations. Now, Patrick and Giustino have shown that quantum nuclear dynamics of carbon atoms must be taken into consideration when explaining electronic and optical properties. 12 June 2013 | doi: 10.1038/ncomms3006 Physical Sciences  Materials science  Nanotechnology  Optical physics  Solution-based circuits enable rapid and multiplexed pathogen detection Brian Lam, Jagotamoy Das, Richard D. Holmes, Ludovic Live, Andrew Sage, Edward H. Sargent and Shana O. Kelley Rapid, highly multiplexed molecular detection platforms may enable more specific and effective disease diagnosis. Here, a solution-based circuit is reported that enables the analysis of samples for panels of pathogens and antibiotic-resistance profiles at clinically relevant levels in less than 2 min. 12 June 2013 | doi: 10.1038/ncomms3001 Chemical Sciences  Analytical chemistry  Medicinal chemistry  Nanotechnology  Comparative cross-linking and mass spectrometry of an intact F-type ATPase suggest a role for phosphorylation OPEN Carla Schmidt, Min Zhou, Hazel Marriott, Nina Morgner, Argyris Politis and Carol V. Robinson Rotary ATPases are membrane-embedded motors that produce or consume ATP and control pH within cells. Schmidt et al. use mass spectrometry to characterize the intact chloroplast ATPase from spinach and, using comparative cross-linking, show that phosphorylation affects stability and nucleotide occupancy. 12 June 2013 | doi: 10.1038/ncomms2985 Biological Sciences  Biochemistry  Biophysics  Chemical biology  Integrating DNA strand-displacement circuitry with DNA tile self-assembly OPEN David Yu Zhang, Rizal F. Hariadi, Harry M.T. Choi and Erik Winfree DNA tile self-assembly and DNA strand displacement circuits are well-developed frameworks in DNA nanotechnology. Here, the two approaches are combined to give programmable kinetic control of DNA nanotube self-assembly. 12 June 2013 | doi: 10.1038/ncomms2965 Chemical Sciences  Nanotechnology    Nature Communications JOBS of the week Data Scientist Harvard Medical School Research Fellowship Faculty of Medicine, University of Porto Research Technician EMBL (European Molecular Biology Laboratory) Postdoctoral Scientist University of Oxford Postdoctoral Fellow Cancer Science Institute of Singapore Postdoctoral Research Fellow University of Saskatchewan (U of S) Post Doctoral Research Associate King's College London Assistant, Associate or Full Professor School of Earth Sciences, Stanford University Post Doctoral Fellow Georg August University Goettingen Research Assistant Cambridge Institute for Medical Research More Science jobs from Nature Communications EVENT qPCR & Digital PCR Congress 09.-10.09.13 Lyon, France More science events from       Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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